[phenixbb] Error in PDB Validation letter

[Raja Dey]

Hi,
    I am getting two errors in pdb validation report as follows:
I think I need to use B-DNA constraint in the refinement. This is a 2.4 A data. How can I do that in PHENIX in cammand line promt.

Another thing is, I have a small molecule in the complex, which I called as BML. I think that's might be the problem. This is known as BML210. What I should call this compound? Should I also give a chain ID for this compound? See the errors given below.

    *** Covalent Angle Values:

    The overall RMS deviation for covalent angles relative to the standard 
    dictionary is    1.4 degrees.

    The following table contains a list of the covalent bond angles
    greater than 6 times standard deviation.


 Deviation  Residue  Chain  Sequence  AT1  -  AT2  -  AT3    Bond    Dictionary  Standard
             Name     ID     Number                          Angle      Value    Deviation
-------------------------------------------------------------------------------------------
    -4.8     DA       E        1      C1'  -  C2'  -  C3'     97.6     102.4        0.8
    -5.8     DA       E        2      C1'  -  C2'  -  C3'     96.6     102.4        0.8
     3.3     DA       E        2      N9   -  C1'  -  O4'    111.6     108.3        0.3
    -5.0     DC       E        5      N1   -  C1'  -  O4'    103.0     108.0        0.7
    -5.1     DT       E        6      C1'  -  C2'  -  C3'     97.3     102.4        0.8
    -6.7     DT       E        8      C1'  -  O4'  -  C4'    103.4     110.1        1.0
     2.3     DT       E        8      N1   -  C1'  -  O4'    110.6     108.3        0.3
    -4.5     DT       E       11      N1   -  C1'  -  O4'    103.5     108.0        0.7
    -6.1     DA       F        2      C1'  -  C2'  -  C3'     96.3     102.4        0.8
     3.0     DA       F        2      N9   -  C1'  -  O4'    111.3     108.3        0.3
    -5.3     DC       F        5      N1   -  C1'  -  O4'    102.7     108.0        0.7
    -4.9     DT       F        6      C1'  -  C2'  -  C3'     97.5     102.4        0.8
    -4.5     DA       F       10      N9   -  C1'  -  O4'    103.5     108.0        0.7
    -7.8     DA       F       11      N9   -  C1'  -  O4'    100.2     108.0        0.7



==> The following residues have extra atoms:                         
    
     RES MOD#C SEQ          ATOMS
    
     BML(      100)          N1  C10  C11  C12  C13  C14  C15  C16  C17  C18 
                            C19   O2   N2  C20   N3   C7   C8   C9 




ERROR: dissociated residue(s):
	BML  100


Raja